Starting phenix.real_space_refine on Sun Sep 13 20:40:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s5u_54610/09_2026/9s5u_54610.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s5u_54610/09_2026/9s5u_54610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s5u_54610/09_2026/9s5u_54610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s5u_54610/09_2026/9s5u_54610.map" model { file = "/net/cci-nas-00/data/ceres_data/9s5u_54610/09_2026/9s5u_54610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s5u_54610/09_2026/9s5u_54610.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16113 2.51 5 N 4054 2.21 5 O 4707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24982 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5775 Classifications: {'peptide': 713} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 680} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2378 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "C" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1616 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1509 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 178} Chain: "E" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1086 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1348 Classifications: {'peptide': 167} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 158} Chain: "H" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1096 Classifications: {'peptide': 142} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "I" Number of atoms: 9174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9174 Classifications: {'peptide': 1172} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1112} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 85 Unusual residues: {'AJP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.01, per 1000 atoms: 0.20 Number of scatterers: 24982 At special positions: 0 Unit cell: (120.019, 178.752, 179.603, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4707 8.00 N 4054 7.00 C 16113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A 801 " - " ASN A 574 " " NAG A 802 " - " ASN A 202 " " NAG A 803 " - " ASN A 192 " " NAG G 301 " - " ASN G 67 " " NAG G 302 " - " ASN G 97 " " NAG Z 1 " - " ASN A 73 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 964.2 milliseconds 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5916 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 29 sheets defined 44.7% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 248 through 270 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 644 through 649 Processing helix chain 'A' and resid 726 through 757 removed outlier: 4.125A pdb=" N LEU A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Proline residue: A 746 - end of helix removed outlier: 3.530A pdb=" N TRP A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 16 Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.572A pdb=" N THR B 20 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE B 22 " --> pdb=" O TYR B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 41 Processing helix chain 'B' and resid 46 through 64 Processing helix chain 'B' and resid 67 through 81 Processing helix chain 'B' and resid 85 through 100 removed outlier: 3.861A pdb=" N ASN B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 116 removed outlier: 3.580A pdb=" N ALA B 105 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 141 removed outlier: 3.562A pdb=" N TYR B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 159 Processing helix chain 'B' and resid 162 through 175 removed outlier: 4.213A pdb=" N TRP B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 3.662A pdb=" N ALA B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 214 removed outlier: 3.611A pdb=" N PHE B 200 " --> pdb=" O ASN B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 236 removed outlier: 3.536A pdb=" N THR B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLU B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 254 Processing helix chain 'B' and resid 261 through 277 Processing helix chain 'B' and resid 278 through 292 removed outlier: 3.814A pdb=" N LYS B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.969A pdb=" N TYR C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 34 Processing helix chain 'C' and resid 43 through 63 removed outlier: 3.731A pdb=" N ALA C 56 " --> pdb=" O TYR C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 84 Processing helix chain 'C' and resid 112 through 140 Proline residue: C 128 - end of helix removed outlier: 3.542A pdb=" N PHE C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 156 through 161 removed outlier: 3.834A pdb=" N GLN C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 4.446A pdb=" N TRP C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 220 through 232 removed outlier: 4.622A pdb=" N HIS C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA C 227 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 removed outlier: 3.904A pdb=" N GLU C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 14 Processing helix chain 'D' and resid 18 through 22 Processing helix chain 'D' and resid 46 through 78 removed outlier: 4.729A pdb=" N LEU D 59 " --> pdb=" O GLN D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 82 Processing helix chain 'D' and resid 83 through 94 removed outlier: 3.642A pdb=" N PHE D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 119 Proline residue: D 113 - end of helix Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.536A pdb=" N ALA D 123 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 162 Processing helix chain 'D' and resid 168 through 176 removed outlier: 3.571A pdb=" N TRP D 172 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU D 173 " --> pdb=" O GLY D 170 " (cutoff:3.500A) Proline residue: D 174 - end of helix Processing helix chain 'E' and resid 2 through 32 removed outlier: 3.592A pdb=" N LYS E 6 " --> pdb=" O SER E 2 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 32 " --> pdb=" O HIS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 38 removed outlier: 3.517A pdb=" N ALA E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 67 removed outlier: 3.874A pdb=" N MET E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 99 through 106 Processing helix chain 'E' and resid 110 through 115 Processing helix chain 'E' and resid 121 through 137 Processing helix chain 'F' and resid 13 through 43 removed outlier: 3.607A pdb=" N LYS F 21 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG F 23 " --> pdb=" O ASP F 19 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU F 24 " --> pdb=" O ASN F 20 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY F 36 " --> pdb=" O ALA F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 68 Processing helix chain 'F' and resid 72 through 77 removed outlier: 4.197A pdb=" N PHE F 76 " --> pdb=" O GLN F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 85 removed outlier: 3.534A pdb=" N PHE F 85 " --> pdb=" O LEU F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 108 removed outlier: 3.710A pdb=" N VAL F 97 " --> pdb=" O ILE F 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 157 Processing helix chain 'G' and resid 158 through 167 Processing helix chain 'H' and resid 123 through 133 Processing helix chain 'H' and resid 134 through 138 removed outlier: 4.064A pdb=" N THR H 137 " --> pdb=" O ASP H 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 45 Processing helix chain 'I' and resid 53 through 74 removed outlier: 3.534A pdb=" N THR I 57 " --> pdb=" O GLY I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 77 No H-bonds generated for 'chain 'I' and resid 75 through 77' Processing helix chain 'I' and resid 78 through 86 Processing helix chain 'I' and resid 156 through 163 removed outlier: 3.996A pdb=" N PHE I 160 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 177 Processing helix chain 'I' and resid 188 through 197 Processing helix chain 'I' and resid 199 through 215 removed outlier: 3.588A pdb=" N VAL I 209 " --> pdb=" O GLN I 205 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP I 215 " --> pdb=" O LEU I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 248 removed outlier: 3.553A pdb=" N THR I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 338 removed outlier: 3.690A pdb=" N LYS I 335 " --> pdb=" O GLY I 332 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE I 336 " --> pdb=" O VAL I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 375 Processing helix chain 'I' and resid 376 through 387 Processing helix chain 'I' and resid 392 through 395 removed outlier: 4.007A pdb=" N ASP I 395 " --> pdb=" O VAL I 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 392 through 395' Processing helix chain 'I' and resid 396 through 425 removed outlier: 3.584A pdb=" N PHE I 409 " --> pdb=" O PHE I 405 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR I 416 " --> pdb=" O ILE I 412 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS I 423 " --> pdb=" O VAL I 419 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET I 424 " --> pdb=" O GLU I 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 427 through 443 removed outlier: 4.117A pdb=" N ILE I 439 " --> pdb=" O CYS I 435 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL I 443 " --> pdb=" O ILE I 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 449 through 465 removed outlier: 3.878A pdb=" N MET I 453 " --> pdb=" O MET I 449 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE I 465 " --> pdb=" O ALA I 461 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 479 Processing helix chain 'I' and resid 522 through 532 Processing helix chain 'I' and resid 546 through 557 Processing helix chain 'I' and resid 606 through 614 removed outlier: 4.625A pdb=" N GLU I 612 " --> pdb=" O GLU I 608 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG I 613 " --> pdb=" O THR I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 621 through 631 removed outlier: 3.600A pdb=" N SER I 631 " --> pdb=" O SER I 627 " (cutoff:3.500A) Processing helix chain 'I' and resid 647 through 652 Processing helix chain 'I' and resid 655 through 660 removed outlier: 3.556A pdb=" N GLU I 660 " --> pdb=" O ARG I 656 " (cutoff:3.500A) Processing helix chain 'I' and resid 681 through 689 Processing helix chain 'I' and resid 700 through 712 Processing helix chain 'I' and resid 767 through 773 Processing helix chain 'I' and resid 778 through 784 Processing helix chain 'I' and resid 793 through 806 Processing helix chain 'I' and resid 820 through 826 removed outlier: 3.948A pdb=" N GLN I 826 " --> pdb=" O GLY I 822 " (cutoff:3.500A) Processing helix chain 'I' and resid 836 through 868 removed outlier: 3.568A pdb=" N LEU I 841 " --> pdb=" O THR I 837 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN I 868 " --> pdb=" O MET I 864 " (cutoff:3.500A) Processing helix chain 'I' and resid 890 through 899 Processing helix chain 'I' and resid 903 through 915 Processing helix chain 'I' and resid 971 through 1013 removed outlier: 4.193A pdb=" N THR I 975 " --> pdb=" O VAL I 971 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE I 978 " --> pdb=" O VAL I 974 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU I 985 " --> pdb=" O GLY I 981 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL I 986 " --> pdb=" O ARG I 982 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR I 988 " --> pdb=" O ALA I 984 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE I 989 " --> pdb=" O LEU I 985 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA I 996 " --> pdb=" O TYR I 992 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU I 997 " --> pdb=" O LYS I 993 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU I1000 " --> pdb=" O ALA I 996 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER I1002 " --> pdb=" O ASN I 998 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR I1004 " --> pdb=" O LEU I1000 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA I1012 " --> pdb=" O ILE I1008 " (cutoff:3.500A) Processing helix chain 'I' and resid 1017 through 1035 Processing helix chain 'I' and resid 1055 through 1084 removed outlier: 3.711A pdb=" N THR I1072 " --> pdb=" O VAL I1068 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1120 removed outlier: 3.892A pdb=" N ALA I1118 " --> pdb=" O VAL I1114 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN I1120 " --> pdb=" O THR I1116 " (cutoff:3.500A) Processing helix chain 'I' and resid 1134 through 1152 Processing helix chain 'I' and resid 1155 through 1162 removed outlier: 3.527A pdb=" N ASN I1159 " --> pdb=" O LEU I1155 " (cutoff:3.500A) Processing helix chain 'I' and resid 1168 through 1197 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 48 removed outlier: 3.767A pdb=" N LYS A 45 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N CYS A 67 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL A 84 " --> pdb=" O CYS A 67 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 69 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG A 82 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER A 71 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 78 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 127 removed outlier: 6.521A pdb=" N LEU A 122 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP A 116 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 124 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ALA A 101 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP A 95 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 180 removed outlier: 6.809A pdb=" N VAL A 188 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 179 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ALA A 186 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TRP A 210 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N SER A 200 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASN A 202 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 219 through 226 removed outlier: 3.680A pdb=" N ASP A 221 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TRP A 324 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP A 315 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 322 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 333 through 338 removed outlier: 6.904A pdb=" N PHE A 349 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET A 336 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 347 " --> pdb=" O MET A 336 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP A 338 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLU A 345 " --> pdb=" O TRP A 338 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 369 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU A 359 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE A 367 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 379 through 384 Processing sheet with id=AA9, first strand: chain 'A' and resid 445 through 453 removed outlier: 6.575A pdb=" N GLY A 438 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS A 451 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE A 436 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 426 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE A 427 " --> pdb=" O PHE D 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 458 through 465 removed outlier: 6.646A pdb=" N LEU A 496 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR A 463 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA A 494 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LYS A 465 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU A 492 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 519 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASP A 511 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 517 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU H 107 " --> pdb=" O THR A 520 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 477 Processing sheet with id=AB3, first strand: chain 'A' and resid 534 through 537 removed outlier: 3.593A pdb=" N GLN A 555 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 604 through 609 Processing sheet with id=AB5, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.854A pdb=" N MET C 146 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 72 through 73 Processing sheet with id=AB7, first strand: chain 'G' and resid 55 through 61 removed outlier: 5.683A pdb=" N GLY G 5 " --> pdb=" O ASN G 59 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 43 through 46 removed outlier: 3.951A pdb=" N TYR G 71 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG G 87 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 31 through 38 removed outlier: 6.855A pdb=" N THR H 20 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ILE H 38 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LEU H 18 " --> pdb=" O ILE H 38 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR H 8 " --> pdb=" O PRO H 17 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY H 45 " --> pdb=" O MET H 65 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET H 65 " --> pdb=" O GLY H 45 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR H 47 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER H 63 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU H 49 " --> pdb=" O CYS H 61 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 85 through 92 removed outlier: 6.944A pdb=" N ASP H 78 " --> pdb=" O LYS H 86 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL H 88 " --> pdb=" O ILE H 76 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE H 76 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU H 90 " --> pdb=" O ASP H 74 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP H 74 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 7 through 8 Processing sheet with id=AC3, first strand: chain 'I' and resid 12 through 18 removed outlier: 3.684A pdb=" N ASP I 14 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS I 98 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 256 through 260 Processing sheet with id=AC5, first strand: chain 'I' and resid 277 through 280 removed outlier: 6.437A pdb=" N LEU I 366 " --> pdb=" O LEU I 296 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP I 292 " --> pdb=" O THR I 370 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 310 through 316 removed outlier: 6.631A pdb=" N THR I 312 " --> pdb=" O GLU I 304 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU I 304 " --> pdb=" O THR I 312 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER I 299 " --> pdb=" O VAL I 348 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL I 348 " --> pdb=" O SER I 299 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE I 301 " --> pdb=" O LEU I 346 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 467 through 469 Processing sheet with id=AC8, first strand: chain 'I' and resid 692 through 695 Processing sheet with id=AC9, first strand: chain 'I' and resid 498 through 503 removed outlier: 6.714A pdb=" N ILE I 670 " --> pdb=" O GLU I 500 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU I 502 " --> pdb=" O PHE I 668 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE I 668 " --> pdb=" O LEU I 502 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU I 638 " --> pdb=" O ASN I 666 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE I 668 " --> pdb=" O LEU I 636 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU I 636 " --> pdb=" O PHE I 668 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE I 670 " --> pdb=" O ARG I 634 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG I 634 " --> pdb=" O ILE I 670 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER I 594 " --> pdb=" O ILE I 576 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE I 576 " --> pdb=" O SER I 594 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 536 through 537 Processing sheet with id=AD2, first strand: chain 'I' and resid 742 through 745 removed outlier: 3.507A pdb=" N THR I 766 " --> pdb=" O LEU I 721 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ARG I 723 " --> pdb=" O THR I 766 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N ALA I 790 " --> pdb=" O ILE I 763 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL I 765 " --> pdb=" O ALA I 790 " (cutoff:3.500A) 1215 hydrogen bonds defined for protein. 3522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.35 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5774 1.33 - 1.45: 5293 1.45 - 1.57: 14282 1.57 - 1.70: 0 1.70 - 1.82: 189 Bond restraints: 25538 Sorted by residual: bond pdb=" C4 NAG A 802 " pdb=" O4 NAG A 802 " ideal model delta sigma weight residual 1.409 1.347 0.062 2.00e-02 2.50e+03 9.46e+00 bond pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.21e-02 6.83e+03 7.14e+00 bond pdb=" N PHE A 72 " pdb=" CA PHE A 72 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.21e-02 6.83e+03 6.62e+00 bond pdb=" N ASN A 73 " pdb=" CA ASN A 73 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.24e-02 6.50e+03 4.40e+00 bond pdb=" C65 AJP I1301 " pdb=" O64 AJP I1301 " ideal model delta sigma weight residual 1.373 1.409 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 25533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 34172 2.23 - 4.45: 408 4.45 - 6.68: 56 6.68 - 8.91: 17 8.91 - 11.13: 4 Bond angle restraints: 34657 Sorted by residual: angle pdb=" N VAL I 198 " pdb=" CA VAL I 198 " pdb=" C VAL I 198 " ideal model delta sigma weight residual 111.91 107.98 3.93 8.90e-01 1.26e+00 1.95e+01 angle pdb=" C MET I 74 " pdb=" CA MET I 74 " pdb=" CB MET I 74 " ideal model delta sigma weight residual 112.38 103.90 8.48 2.17e+00 2.12e-01 1.53e+01 angle pdb=" C SER A 71 " pdb=" N PHE A 72 " pdb=" CA PHE A 72 " ideal model delta sigma weight residual 122.99 117.74 5.25 1.41e+00 5.03e-01 1.39e+01 angle pdb=" CB MET D 152 " pdb=" CG MET D 152 " pdb=" SD MET D 152 " ideal model delta sigma weight residual 112.70 123.83 -11.13 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CB MET I 449 " pdb=" CG MET I 449 " pdb=" SD MET I 449 " ideal model delta sigma weight residual 112.70 123.15 -10.45 3.00e+00 1.11e-01 1.21e+01 ... (remaining 34652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13268 17.94 - 35.88: 1719 35.88 - 53.82: 479 53.82 - 71.76: 82 71.76 - 89.70: 28 Dihedral angle restraints: 15576 sinusoidal: 6445 harmonic: 9131 Sorted by residual: dihedral pdb=" CA ILE I1053 " pdb=" C ILE I1053 " pdb=" N PHE I1054 " pdb=" CA PHE I1054 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA LEU I 73 " pdb=" C LEU I 73 " pdb=" N MET I 74 " pdb=" CA MET I 74 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ALA I 478 " pdb=" C ALA I 478 " pdb=" N GLY I 479 " pdb=" CA GLY I 479 " ideal model delta harmonic sigma weight residual 180.00 158.83 21.17 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 15573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.269: 3995 0.269 - 0.538: 1 0.538 - 0.807: 0 0.807 - 1.075: 0 1.075 - 1.344: 2 Chirality restraints: 3998 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN A 73 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.06 -1.34 2.00e-01 2.50e+01 4.52e+01 chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 574 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.31 -1.09 2.00e-01 2.50e+01 2.97e+01 chirality pdb=" C1 NAG G 302 " pdb=" ND2 ASN G 97 " pdb=" C2 NAG G 302 " pdb=" O5 NAG G 302 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 ... (remaining 3995 not shown) Planarity restraints: 4365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 574 " 0.233 2.00e-02 2.50e+03 2.64e-01 8.72e+02 pdb=" CG ASN A 574 " -0.128 2.00e-02 2.50e+03 pdb=" OD1 ASN A 574 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 574 " -0.424 2.00e-02 2.50e+03 pdb=" C1 NAG A 801 " 0.314 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 803 " 0.314 2.00e-02 2.50e+03 2.62e-01 8.55e+02 pdb=" C7 NAG A 803 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 803 " 0.190 2.00e-02 2.50e+03 pdb=" N2 NAG A 803 " -0.447 2.00e-02 2.50e+03 pdb=" O7 NAG A 803 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 73 " -0.173 2.00e-02 2.50e+03 2.13e-01 5.70e+02 pdb=" CG ASN A 73 " 0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN A 73 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 73 " 0.356 2.00e-02 2.50e+03 pdb=" C1 NAG Z 1 " -0.257 2.00e-02 2.50e+03 ... (remaining 4362 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1048 2.72 - 3.27: 24532 3.27 - 3.81: 39440 3.81 - 4.36: 45133 4.36 - 4.90: 78256 Nonbonded interactions: 188409 Sorted by model distance: nonbonded pdb=" O SER A 526 " pdb=" OG SER A 526 " model vdw 2.176 3.040 nonbonded pdb=" O PHE I 6 " pdb=" N PHE I 144 " model vdw 2.215 3.120 nonbonded pdb=" OE2 GLU B 272 " pdb=" NZ LYS B 276 " model vdw 2.220 3.120 nonbonded pdb=" OD1 ASN I1129 " pdb=" OG SER I1132 " model vdw 2.241 3.040 nonbonded pdb=" OE1 GLN I1112 " pdb=" OD2 ASP I1182 " model vdw 2.244 3.040 ... (remaining 188404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.040 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 25545 Z= 0.148 Angle : 0.642 18.422 34678 Z= 0.329 Chirality : 0.051 1.344 3998 Planarity : 0.006 0.262 4359 Dihedral : 17.427 89.700 9660 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 1.09 % Allowed : 31.11 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 3085 helix: 1.43 (0.15), residues: 1250 sheet: 0.43 (0.23), residues: 514 loop : -1.54 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 383 TYR 0.019 0.001 TYR H 92 PHE 0.015 0.001 PHE I 149 TRP 0.022 0.001 TRP I1187 HIS 0.005 0.001 HIS E 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (25538) covalent geometry : angle 0.62404 / 0.32 (34657) hydrogen bonds : bond 0.14540 / 9.27 ( 1215) hydrogen bonds : angle 5.80282 / 4.13 ( 3522) link_BETA1-4 : bond 0.00764 / 0.40 ( 1) link_BETA1-4 : angle 1.23410 / 0.68 ( 3) link_NAG-ASN : bond 0.03752 / 1.86 ( 6) link_NAG-ASN : angle 6.62331 / 3.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 612 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 SER cc_start: 0.8771 (m) cc_final: 0.8233 (t) REVERT: A 217 THR cc_start: 0.8333 (p) cc_final: 0.8048 (m) REVERT: A 316 MET cc_start: 0.8259 (mtp) cc_final: 0.8028 (mtm) REVERT: A 335 LYS cc_start: 0.8304 (mmtp) cc_final: 0.8103 (mmtm) REVERT: A 457 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7481 (mmmt) REVERT: A 480 ASP cc_start: 0.7457 (t0) cc_final: 0.7183 (t0) REVERT: A 500 GLU cc_start: 0.7232 (pm20) cc_final: 0.6573 (pm20) REVERT: A 550 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6723 (mt-10) REVERT: A 744 ILE cc_start: 0.8522 (mm) cc_final: 0.7878 (tt) REVERT: B 136 ILE cc_start: 0.8063 (mm) cc_final: 0.7794 (mt) REVERT: C 2 LEU cc_start: 0.8626 (tp) cc_final: 0.8401 (tt) REVERT: C 26 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7716 (ttmm) REVERT: D 12 HIS cc_start: 0.8181 (m170) cc_final: 0.7739 (m-70) REVERT: D 22 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: D 93 MET cc_start: 0.6333 (mmm) cc_final: 0.5876 (tmm) REVERT: D 143 MET cc_start: 0.7188 (mtm) cc_final: 0.6889 (mtm) REVERT: E 127 LYS cc_start: 0.8045 (tttt) cc_final: 0.7645 (tttt) REVERT: F 93 ILE cc_start: 0.8142 (tt) cc_final: 0.7921 (tp) REVERT: G 4 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7840 (mmt180) REVERT: G 135 THR cc_start: 0.8519 (m) cc_final: 0.8049 (p) REVERT: I 215 ASP cc_start: 0.7295 (m-30) cc_final: 0.6977 (m-30) REVERT: I 245 GLU cc_start: 0.7265 (tp30) cc_final: 0.6924 (tp30) REVERT: I 260 ARG cc_start: 0.7461 (tpp80) cc_final: 0.7207 (tpp80) REVERT: I 430 LYS cc_start: 0.7645 (mptt) cc_final: 0.7328 (mmtm) REVERT: I 549 GLU cc_start: 0.7397 (mp0) cc_final: 0.6670 (tt0) REVERT: I 625 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6572 (p90) REVERT: I 646 MET cc_start: 0.4530 (pmm) cc_final: 0.4023 (ppp) REVERT: I 773 LEU cc_start: 0.7309 (mt) cc_final: 0.6998 (tt) REVERT: I 774 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7282 (mm-30) REVERT: I 853 MET cc_start: 0.7268 (tmm) cc_final: 0.6823 (tmm) REVERT: I 859 LYS cc_start: 0.7136 (tptt) cc_final: 0.6788 (pttm) REVERT: I 1065 GLN cc_start: 0.7403 (mt0) cc_final: 0.7171 (mt0) REVERT: I 1127 ARG cc_start: 0.7167 (mtp-110) cc_final: 0.6272 (mtp180) REVERT: I 1129 ASN cc_start: 0.6490 (p0) cc_final: 0.6183 (p0) REVERT: I 1136 MET cc_start: 0.6414 (mmm) cc_final: 0.5927 (mmm) outliers start: 30 outliers final: 24 residues processed: 624 average time/residue: 0.1726 time to fit residues: 171.8572 Evaluate side-chains 615 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 589 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 237 PHE Chi-restraints excluded: chain I residue 275 MET Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 449 MET Chi-restraints excluded: chain I residue 625 TYR Chi-restraints excluded: chain I residue 695 MET Chi-restraints excluded: chain I residue 734 PHE Chi-restraints excluded: chain I residue 803 THR Chi-restraints excluded: chain I residue 1117 PHE Chi-restraints excluded: chain I residue 1191 HIS Chi-restraints excluded: chain I residue 1196 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.0370 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.0170 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 390 HIS ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 62 ASN D 148 GLN D 186 GLN E 28 HIS E 88 ASN F 10 GLN F 12 ASN G 103 ASN H 96 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 980 GLN ** I1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1113 GLN I1133 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.157215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116763 restraints weight = 40955.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114915 restraints weight = 28622.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116062 restraints weight = 24414.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116548 restraints weight = 19902.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116950 restraints weight = 16660.763| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25545 Z= 0.200 Angle : 0.618 9.324 34678 Z= 0.322 Chirality : 0.045 0.410 3998 Planarity : 0.004 0.053 4359 Dihedral : 6.602 69.737 3727 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.98 % Rotamer: Outliers : 4.97 % Allowed : 25.55 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 3085 helix: 1.55 (0.15), residues: 1267 sheet: 0.46 (0.23), residues: 522 loop : -1.59 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 55 TYR 0.021 0.002 TYR G 75 PHE 0.018 0.001 PHE F 26 TRP 0.017 0.002 TRP I1187 HIS 0.008 0.001 HIS I1069 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (25538) covalent geometry : angle 0.61382 / 0.32 (34657) hydrogen bonds : bond 0.06180 / 4.13 ( 1215) hydrogen bonds : angle 4.71416 / 3.33 ( 3522) link_BETA1-4 : bond 0.00295 / 0.16 ( 1) link_BETA1-4 : angle 1.52457 / 0.84 ( 3) link_NAG-ASN : bond 0.00540 / 0.23 ( 6) link_NAG-ASN : angle 3.09180 / 1.87 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 604 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 THR cc_start: 0.8239 (p) cc_final: 0.7965 (m) REVERT: A 335 LYS cc_start: 0.8273 (mmtp) cc_final: 0.8066 (mmtm) REVERT: A 457 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7460 (mmmt) REVERT: A 460 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7316 (tmm) REVERT: A 480 ASP cc_start: 0.7473 (t0) cc_final: 0.7167 (t0) REVERT: A 500 GLU cc_start: 0.7244 (pm20) cc_final: 0.6657 (pm20) REVERT: A 594 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7616 (mm-40) REVERT: A 744 ILE cc_start: 0.8601 (mm) cc_final: 0.7949 (tt) REVERT: B 136 ILE cc_start: 0.8182 (mm) cc_final: 0.7934 (mt) REVERT: C 26 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7786 (ttmm) REVERT: C 143 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7783 (p90) REVERT: C 156 PHE cc_start: 0.8440 (m-80) cc_final: 0.8206 (m-80) REVERT: C 158 GLU cc_start: 0.7633 (mp0) cc_final: 0.7123 (mp0) REVERT: D 12 HIS cc_start: 0.8219 (m170) cc_final: 0.7766 (m-70) REVERT: D 25 GLN cc_start: 0.7086 (mp10) cc_final: 0.6702 (mp10) REVERT: D 93 MET cc_start: 0.6374 (mmm) cc_final: 0.5678 (tmm) REVERT: D 143 MET cc_start: 0.7220 (mtm) cc_final: 0.6839 (mtm) REVERT: E 127 LYS cc_start: 0.8072 (tttt) cc_final: 0.7692 (tttt) REVERT: F 58 ASN cc_start: 0.8173 (m-40) cc_final: 0.7908 (m-40) REVERT: F 93 ILE cc_start: 0.8139 (tt) cc_final: 0.7881 (tp) REVERT: G 4 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7761 (mmt180) REVERT: G 135 THR cc_start: 0.8533 (m) cc_final: 0.8236 (p) REVERT: H 61 CYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7104 (t) REVERT: H 86 LYS cc_start: 0.7686 (mtpt) cc_final: 0.7443 (mtpp) REVERT: I 82 LYS cc_start: 0.7812 (pttm) cc_final: 0.7575 (pttm) REVERT: I 206 VAL cc_start: 0.7457 (m) cc_final: 0.7065 (t) REVERT: I 215 ASP cc_start: 0.7414 (m-30) cc_final: 0.7080 (m-30) REVERT: I 244 LYS cc_start: 0.8124 (tppt) cc_final: 0.7775 (tppt) REVERT: I 260 ARG cc_start: 0.7482 (tpp80) cc_final: 0.7204 (tpp80) REVERT: I 680 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.7012 (mt) REVERT: I 780 ARG cc_start: 0.6289 (tpp-160) cc_final: 0.5968 (ttm170) REVERT: I 781 ASP cc_start: 0.7459 (t0) cc_final: 0.7253 (t70) REVERT: I 801 LEU cc_start: 0.7148 (tt) cc_final: 0.6626 (tp) REVERT: I 843 LYS cc_start: 0.8004 (mmtm) cc_final: 0.7541 (mmtm) REVERT: I 849 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.7537 (ptp-110) REVERT: I 853 MET cc_start: 0.7494 (tmm) cc_final: 0.7184 (tmm) REVERT: I 859 LYS cc_start: 0.7130 (tptt) cc_final: 0.6719 (pttm) REVERT: I 975 THR cc_start: 0.8267 (p) cc_final: 0.7876 (t) REVERT: I 1082 LYS cc_start: 0.7031 (tppt) cc_final: 0.6646 (ttmm) REVERT: I 1127 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6391 (mtp180) REVERT: I 1129 ASN cc_start: 0.6232 (p0) cc_final: 0.5986 (p0) outliers start: 137 outliers final: 90 residues processed: 676 average time/residue: 0.1635 time to fit residues: 177.5449 Evaluate side-chains 687 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 591 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 175 TRP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain F residue 10 GLN Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 61 CYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 237 PHE Chi-restraints excluded: chain I residue 271 GLU Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 308 SER Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 469 CYS Chi-restraints excluded: chain I residue 680 ILE Chi-restraints excluded: chain I residue 695 MET Chi-restraints excluded: chain I residue 824 LEU Chi-restraints excluded: chain I residue 965 THR Chi-restraints excluded: chain I residue 983 CYS Chi-restraints excluded: chain I residue 988 THR Chi-restraints excluded: chain I residue 1028 LEU Chi-restraints excluded: chain I residue 1032 PHE Chi-restraints excluded: chain I residue 1061 SER Chi-restraints excluded: chain I residue 1112 GLN Chi-restraints excluded: chain I residue 1117 PHE Chi-restraints excluded: chain I residue 1127 ARG Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1163 LYS Chi-restraints excluded: chain I residue 1196 PHE Chi-restraints excluded: chain I residue 1198 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 153 optimal weight: 0.3980 chunk 242 optimal weight: 40.0000 chunk 68 optimal weight: 0.0010 chunk 291 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.4364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 670 ASN C 62 ASN E 28 HIS E 88 ASN F 10 GLN H 96 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 776 HIS I 785 HIS I 990 GLN ** I1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1133 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.158367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118307 restraints weight = 40801.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115407 restraints weight = 31498.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116597 restraints weight = 27319.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117290 restraints weight = 21530.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118147 restraints weight = 18144.684| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25545 Z= 0.120 Angle : 0.555 9.261 34678 Z= 0.287 Chirality : 0.042 0.392 3998 Planarity : 0.004 0.048 4359 Dihedral : 5.710 58.589 3694 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.88 % Rotamer: Outliers : 4.43 % Allowed : 26.46 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.15), residues: 3085 helix: 1.79 (0.15), residues: 1270 sheet: 0.56 (0.23), residues: 512 loop : -1.54 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 55 TYR 0.015 0.001 TYR I1075 PHE 0.012 0.001 PHE H 62 TRP 0.016 0.001 TRP I1187 HIS 0.013 0.001 HIS I1069 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (25538) covalent geometry : angle 0.55120 / 0.29 (34657) hydrogen bonds : bond 0.05001 / 3.35 ( 1215) hydrogen bonds : angle 4.46503 / 3.14 ( 3522) link_BETA1-4 : bond 0.00762 / 0.40 ( 1) link_BETA1-4 : angle 1.87593 / 1.04 ( 3) link_NAG-ASN : bond 0.00695 / 0.27 ( 6) link_NAG-ASN : angle 2.87011 / 1.77 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 590 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LYS cc_start: 0.8331 (mmtp) cc_final: 0.8101 (mmtm) REVERT: A 442 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6532 (pm20) REVERT: A 457 LYS cc_start: 0.8100 (mmmt) cc_final: 0.7516 (mmmt) REVERT: A 480 ASP cc_start: 0.7489 (t0) cc_final: 0.7149 (t70) REVERT: A 500 GLU cc_start: 0.7259 (pm20) cc_final: 0.6653 (pm20) REVERT: A 594 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7575 (mm-40) REVERT: A 618 THR cc_start: 0.8331 (m) cc_final: 0.7959 (p) REVERT: A 697 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8132 (m) REVERT: A 744 ILE cc_start: 0.8563 (mm) cc_final: 0.7889 (tt) REVERT: B 136 ILE cc_start: 0.8105 (mm) cc_final: 0.7895 (mt) REVERT: C 26 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7777 (ttmm) REVERT: C 158 GLU cc_start: 0.7658 (mp0) cc_final: 0.7163 (mp0) REVERT: C 225 MET cc_start: 0.5825 (mtm) cc_final: 0.5609 (mmm) REVERT: D 12 HIS cc_start: 0.8160 (m170) cc_final: 0.7683 (m-70) REVERT: D 22 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: D 25 GLN cc_start: 0.7136 (mp10) cc_final: 0.6734 (mp10) REVERT: D 93 MET cc_start: 0.6394 (mmm) cc_final: 0.5687 (tmm) REVERT: D 143 MET cc_start: 0.7120 (mtm) cc_final: 0.6763 (mtm) REVERT: E 127 LYS cc_start: 0.8073 (tttt) cc_final: 0.7689 (tttt) REVERT: F 58 ASN cc_start: 0.8009 (m-40) cc_final: 0.7749 (m-40) REVERT: F 93 ILE cc_start: 0.8108 (tt) cc_final: 0.7813 (tp) REVERT: G 4 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7776 (mmt180) REVERT: G 135 THR cc_start: 0.8538 (m) cc_final: 0.8289 (p) REVERT: H 61 CYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6913 (t) REVERT: H 86 LYS cc_start: 0.7684 (mtpt) cc_final: 0.7368 (mtpp) REVERT: I 82 LYS cc_start: 0.7795 (pttm) cc_final: 0.7540 (pttm) REVERT: I 206 VAL cc_start: 0.7425 (m) cc_final: 0.7065 (t) REVERT: I 215 ASP cc_start: 0.7385 (m-30) cc_final: 0.7075 (m-30) REVERT: I 244 LYS cc_start: 0.8074 (tppt) cc_final: 0.7716 (tptp) REVERT: I 245 GLU cc_start: 0.7243 (tp30) cc_final: 0.6887 (tp30) REVERT: I 260 ARG cc_start: 0.7485 (tpp80) cc_final: 0.7200 (tpp80) REVERT: I 625 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.6574 (p90) REVERT: I 801 LEU cc_start: 0.7050 (tt) cc_final: 0.6561 (tp) REVERT: I 813 MET cc_start: 0.6995 (tmm) cc_final: 0.6733 (tpp) REVERT: I 843 LYS cc_start: 0.7927 (mmtm) cc_final: 0.7425 (mmtm) REVERT: I 849 ARG cc_start: 0.7845 (ttp-110) cc_final: 0.7583 (ptp-110) REVERT: I 853 MET cc_start: 0.7533 (tmm) cc_final: 0.7273 (tmm) REVERT: I 859 LYS cc_start: 0.7112 (tptt) cc_final: 0.6716 (pttm) REVERT: I 974 VAL cc_start: 0.7631 (t) cc_final: 0.7332 (m) REVERT: I 1082 LYS cc_start: 0.6963 (tppt) cc_final: 0.6535 (ttmm) REVERT: I 1193 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.6370 (m-80) outliers start: 122 outliers final: 76 residues processed: 654 average time/residue: 0.1638 time to fit residues: 171.9722 Evaluate side-chains 666 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 583 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 61 CYS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 205 GLN Chi-restraints excluded: chain I residue 237 PHE Chi-restraints excluded: chain I residue 271 GLU Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 469 CYS Chi-restraints excluded: chain I residue 481 ILE Chi-restraints excluded: chain I residue 625 TYR Chi-restraints excluded: chain I residue 695 MET Chi-restraints excluded: chain I residue 705 VAL Chi-restraints excluded: chain I residue 754 HIS Chi-restraints excluded: chain I residue 824 LEU Chi-restraints excluded: chain I residue 988 THR Chi-restraints excluded: chain I residue 1007 SER Chi-restraints excluded: chain I residue 1028 LEU Chi-restraints excluded: chain I residue 1032 PHE Chi-restraints excluded: chain I residue 1112 GLN Chi-restraints excluded: chain I residue 1117 PHE Chi-restraints excluded: chain I residue 1127 ARG Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1191 HIS Chi-restraints excluded: chain I residue 1193 PHE Chi-restraints excluded: chain I residue 1196 PHE Chi-restraints excluded: chain I residue 1198 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 279 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 291 optimal weight: 0.0980 chunk 210 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 390 HIS A 670 ASN B 188 GLN C 62 ASN E 28 HIS E 88 ASN H 96 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1133 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.158084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117693 restraints weight = 40726.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115414 restraints weight = 29971.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116278 restraints weight = 24573.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116931 restraints weight = 20453.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117320 restraints weight = 17661.715| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25545 Z= 0.151 Angle : 0.567 9.281 34678 Z= 0.293 Chirality : 0.043 0.404 3998 Planarity : 0.004 0.048 4359 Dihedral : 5.598 58.477 3688 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 5.08 % Allowed : 25.70 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 3085 helix: 1.84 (0.15), residues: 1275 sheet: 0.53 (0.23), residues: 514 loop : -1.53 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 55 TYR 0.017 0.001 TYR G 75 PHE 0.016 0.001 PHE I 204 TRP 0.017 0.001 TRP I1187 HIS 0.016 0.001 HIS I1069 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (25538) covalent geometry : angle 0.56346 / 0.29 (34657) hydrogen bonds : bond 0.05204 / 3.49 ( 1215) hydrogen bonds : angle 4.40784 / 3.10 ( 3522) link_BETA1-4 : bond 0.00717 / 0.38 ( 1) link_BETA1-4 : angle 1.94040 / 1.07 ( 3) link_NAG-ASN : bond 0.00551 / 0.21 ( 6) link_NAG-ASN : angle 2.82722 / 1.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 596 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LYS cc_start: 0.8306 (mmtp) cc_final: 0.8082 (mmtm) REVERT: A 457 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7456 (mmmt) REVERT: A 460 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7322 (tmm) REVERT: A 480 ASP cc_start: 0.7495 (t0) cc_final: 0.7175 (t70) REVERT: A 500 GLU cc_start: 0.7215 (pm20) cc_final: 0.6674 (pm20) REVERT: A 594 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7582 (mm-40) REVERT: A 697 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8118 (m) REVERT: A 744 ILE cc_start: 0.8544 (mm) cc_final: 0.7871 (tt) REVERT: B 55 GLU cc_start: 0.7755 (tt0) cc_final: 0.7529 (tt0) REVERT: B 118 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7543 (mm-30) REVERT: B 136 ILE cc_start: 0.8186 (mm) cc_final: 0.7951 (mt) REVERT: B 147 SER cc_start: 0.8147 (OUTLIER) cc_final: 0.7796 (p) REVERT: C 26 LYS cc_start: 0.8230 (ttmm) cc_final: 0.7773 (ttmm) REVERT: C 82 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.5762 (tt) REVERT: C 225 MET cc_start: 0.5903 (mtm) cc_final: 0.5246 (mmm) REVERT: D 12 HIS cc_start: 0.8159 (m170) cc_final: 0.7654 (m-70) REVERT: D 22 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.7300 (m-80) REVERT: D 25 GLN cc_start: 0.7121 (mp10) cc_final: 0.6743 (mp10) REVERT: D 93 MET cc_start: 0.6400 (mmm) cc_final: 0.5684 (tmm) REVERT: D 143 MET cc_start: 0.7139 (mtm) cc_final: 0.6790 (mtm) REVERT: E 127 LYS cc_start: 0.8083 (tttt) cc_final: 0.7647 (tttt) REVERT: F 58 ASN cc_start: 0.8053 (m-40) cc_final: 0.7797 (m-40) REVERT: F 93 ILE cc_start: 0.8192 (tt) cc_final: 0.7907 (tp) REVERT: G 4 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7778 (mmt180) REVERT: G 135 THR cc_start: 0.8542 (m) cc_final: 0.8282 (p) REVERT: H 61 CYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6855 (t) REVERT: H 86 LYS cc_start: 0.7683 (mtpt) cc_final: 0.7367 (mtpp) REVERT: H 93 ASP cc_start: 0.7922 (t0) cc_final: 0.7639 (t0) REVERT: I 82 LYS cc_start: 0.7784 (pttm) cc_final: 0.7486 (pttm) REVERT: I 183 ASP cc_start: 0.5512 (p0) cc_final: 0.5291 (p0) REVERT: I 206 VAL cc_start: 0.7458 (m) cc_final: 0.7089 (t) REVERT: I 215 ASP cc_start: 0.7383 (m-30) cc_final: 0.7060 (m-30) REVERT: I 244 LYS cc_start: 0.8114 (tppt) cc_final: 0.7745 (tptp) REVERT: I 260 ARG cc_start: 0.7525 (tpp80) cc_final: 0.7223 (tpp80) REVERT: I 471 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: I 608 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6552 (pm20) REVERT: I 625 TYR cc_start: 0.6886 (OUTLIER) cc_final: 0.6569 (p90) REVERT: I 710 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7112 (pt0) REVERT: I 813 MET cc_start: 0.7068 (tmm) cc_final: 0.6702 (tpp) REVERT: I 843 LYS cc_start: 0.7912 (mmtm) cc_final: 0.7412 (mmtm) REVERT: I 849 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7579 (ptp-110) REVERT: I 853 MET cc_start: 0.7569 (tmm) cc_final: 0.7277 (tmm) REVERT: I 855 MET cc_start: 0.7641 (tmm) cc_final: 0.7412 (tmm) REVERT: I 859 LYS cc_start: 0.7125 (tptt) cc_final: 0.6745 (pttm) REVERT: I 974 VAL cc_start: 0.7620 (t) cc_final: 0.7302 (m) REVERT: I 1082 LYS cc_start: 0.6994 (tppt) cc_final: 0.6557 (ttmm) REVERT: I 1120 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7874 (t0) REVERT: I 1174 LYS cc_start: 0.6739 (mttm) cc_final: 0.6496 (mtmt) REVERT: I 1193 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.6372 (m-80) outliers start: 140 outliers final: 92 residues processed: 671 average time/residue: 0.1662 time to fit residues: 179.0343 Evaluate side-chains 688 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 584 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 61 CYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 205 GLN Chi-restraints excluded: chain I residue 237 PHE Chi-restraints excluded: chain I residue 271 GLU Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain I residue 398 GLU Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 427 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 469 CYS Chi-restraints excluded: chain I residue 471 GLU Chi-restraints excluded: chain I residue 608 GLU Chi-restraints excluded: chain I residue 625 TYR Chi-restraints excluded: chain I residue 695 MET Chi-restraints excluded: chain I residue 705 VAL Chi-restraints excluded: chain I residue 754 HIS Chi-restraints excluded: chain I residue 800 LEU Chi-restraints excluded: chain I residue 824 LEU Chi-restraints excluded: chain I residue 966 SER Chi-restraints excluded: chain I residue 988 THR Chi-restraints excluded: chain I residue 1007 SER Chi-restraints excluded: chain I residue 1028 LEU Chi-restraints excluded: chain I residue 1032 PHE Chi-restraints excluded: chain I residue 1112 GLN Chi-restraints excluded: chain I residue 1117 PHE Chi-restraints excluded: chain I residue 1120 ASN Chi-restraints excluded: chain I residue 1127 ARG Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1186 SER Chi-restraints excluded: chain I residue 1191 HIS Chi-restraints excluded: chain I residue 1193 PHE Chi-restraints excluded: chain I residue 1196 PHE Chi-restraints excluded: chain I residue 1198 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 141 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 276 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 139 optimal weight: 0.0970 chunk 204 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 125 optimal weight: 20.0000 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 670 ASN C 62 ASN E 28 HIS E 88 ASN H 96 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1069 HIS I1112 GLN I1133 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.157950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117290 restraints weight = 40594.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115864 restraints weight = 29839.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116430 restraints weight = 24316.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117074 restraints weight = 20870.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117541 restraints weight = 17870.095| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25545 Z= 0.148 Angle : 0.565 9.213 34678 Z= 0.291 Chirality : 0.043 0.405 3998 Planarity : 0.004 0.066 4359 Dihedral : 5.536 58.291 3687 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 5.30 % Allowed : 25.37 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3085 helix: 1.86 (0.15), residues: 1276 sheet: 0.54 (0.23), residues: 514 loop : -1.54 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 55 TYR 0.017 0.001 TYR G 75 PHE 0.015 0.001 PHE I 204 TRP 0.017 0.001 TRP I1187 HIS 0.005 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (25538) covalent geometry : angle 0.56149 / 0.29 (34657) hydrogen bonds : bond 0.05141 / 3.45 ( 1215) hydrogen bonds : angle 4.35432 / 3.06 ( 3522) link_BETA1-4 : bond 0.00626 / 0.33 ( 1) link_BETA1-4 : angle 2.01270 / 1.10 ( 3) link_NAG-ASN : bond 0.00640 / 0.26 ( 6) link_NAG-ASN : angle 2.65697 / 1.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 588 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LYS cc_start: 0.8281 (mmtp) cc_final: 0.8059 (mmtm) REVERT: A 457 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7495 (mmmt) REVERT: A 460 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7320 (tmm) REVERT: A 480 ASP cc_start: 0.7452 (t0) cc_final: 0.7127 (t70) REVERT: A 500 GLU cc_start: 0.7172 (pm20) cc_final: 0.6690 (pm20) REVERT: A 594 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7570 (mm-40) REVERT: A 697 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8106 (m) REVERT: A 744 ILE cc_start: 0.8562 (mm) cc_final: 0.7885 (tt) REVERT: B 39 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6961 (mtmm) REVERT: B 55 GLU cc_start: 0.7747 (tt0) cc_final: 0.7412 (tt0) REVERT: B 83 GLU cc_start: 0.6959 (mp0) cc_final: 0.6683 (mp0) REVERT: B 118 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7537 (mm-30) REVERT: B 136 ILE cc_start: 0.8224 (mm) cc_final: 0.8005 (mt) REVERT: B 144 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.7726 (p) REVERT: B 147 SER cc_start: 0.8123 (OUTLIER) cc_final: 0.7722 (p) REVERT: C 26 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7787 (ttmm) REVERT: C 82 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5716 (tt) REVERT: C 225 MET cc_start: 0.5790 (mtm) cc_final: 0.5138 (mmm) REVERT: D 12 HIS cc_start: 0.8193 (m170) cc_final: 0.7711 (m-70) REVERT: D 22 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7301 (m-80) REVERT: D 25 GLN cc_start: 0.7135 (mp10) cc_final: 0.6799 (mp10) REVERT: D 93 MET cc_start: 0.6324 (mmm) cc_final: 0.5606 (tmm) REVERT: D 143 MET cc_start: 0.7115 (mtm) cc_final: 0.6770 (mtm) REVERT: E 127 LYS cc_start: 0.8056 (tttt) cc_final: 0.7616 (tttt) REVERT: F 93 ILE cc_start: 0.8239 (tt) cc_final: 0.7960 (tp) REVERT: G 4 ARG cc_start: 0.8122 (mmm160) cc_final: 0.7772 (mmt180) REVERT: G 145 ARG cc_start: 0.8295 (mtp180) cc_final: 0.8048 (mtt180) REVERT: H 61 CYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6792 (t) REVERT: H 86 LYS cc_start: 0.7673 (mtpt) cc_final: 0.7361 (mtpp) REVERT: H 93 ASP cc_start: 0.7920 (t0) cc_final: 0.7609 (t0) REVERT: I 131 GLN cc_start: 0.8014 (tp40) cc_final: 0.7585 (mm-40) REVERT: I 183 ASP cc_start: 0.5534 (p0) cc_final: 0.5278 (p0) REVERT: I 206 VAL cc_start: 0.7430 (m) cc_final: 0.7052 (t) REVERT: I 215 ASP cc_start: 0.7366 (m-30) cc_final: 0.7028 (m-30) REVERT: I 244 LYS cc_start: 0.8079 (tppt) cc_final: 0.7773 (tppt) REVERT: I 245 GLU cc_start: 0.7217 (tp30) cc_final: 0.6851 (tp30) REVERT: I 260 ARG cc_start: 0.7488 (tpp80) cc_final: 0.7205 (tpp80) REVERT: I 471 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7350 (pm20) REVERT: I 608 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6478 (pm20) REVERT: I 625 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.6518 (p90) REVERT: I 801 LEU cc_start: 0.7131 (tt) cc_final: 0.6448 (tp) REVERT: I 807 MET cc_start: 0.7729 (mmm) cc_final: 0.7402 (mmm) REVERT: I 813 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6786 (tpp) REVERT: I 843 LYS cc_start: 0.7866 (mmtm) cc_final: 0.7421 (mmtm) REVERT: I 846 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6524 (tm-30) REVERT: I 849 ARG cc_start: 0.7784 (ttp-110) cc_final: 0.7502 (ptp-110) REVERT: I 853 MET cc_start: 0.7570 (tmm) cc_final: 0.7293 (tmm) REVERT: I 855 MET cc_start: 0.7623 (tmm) cc_final: 0.7339 (tmm) REVERT: I 859 LYS cc_start: 0.7131 (tptt) cc_final: 0.6758 (pttm) REVERT: I 974 VAL cc_start: 0.7561 (t) cc_final: 0.7267 (m) REVERT: I 1082 LYS cc_start: 0.6994 (tppt) cc_final: 0.6578 (ttmm) REVERT: I 1120 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7835 (t0) REVERT: I 1127 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6430 (mtm180) REVERT: I 1174 LYS cc_start: 0.6748 (mttm) cc_final: 0.6449 (mtmt) REVERT: I 1193 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.6513 (m-80) outliers start: 146 outliers final: 97 residues processed: 666 average time/residue: 0.1676 time to fit residues: 178.5306 Evaluate side-chains 699 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 585 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 61 CYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 237 PHE Chi-restraints excluded: chain I residue 271 GLU Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain I residue 398 GLU Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 427 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 469 CYS Chi-restraints excluded: chain I residue 471 GLU Chi-restraints excluded: chain I residue 481 ILE Chi-restraints excluded: chain I residue 608 GLU Chi-restraints excluded: chain I residue 625 TYR Chi-restraints excluded: chain I residue 705 VAL Chi-restraints excluded: chain I residue 754 HIS Chi-restraints excluded: chain I residue 800 LEU Chi-restraints excluded: chain I residue 813 MET Chi-restraints excluded: chain I residue 824 LEU Chi-restraints excluded: chain I residue 846 GLU Chi-restraints excluded: chain I residue 966 SER Chi-restraints excluded: chain I residue 983 CYS Chi-restraints excluded: chain I residue 988 THR Chi-restraints excluded: chain I residue 1000 LEU Chi-restraints excluded: chain I residue 1007 SER Chi-restraints excluded: chain I residue 1028 LEU Chi-restraints excluded: chain I residue 1032 PHE Chi-restraints excluded: chain I residue 1117 PHE Chi-restraints excluded: chain I residue 1120 ASN Chi-restraints excluded: chain I residue 1127 ARG Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1191 HIS Chi-restraints excluded: chain I residue 1193 PHE Chi-restraints excluded: chain I residue 1196 PHE Chi-restraints excluded: chain I residue 1198 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 41 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 243 optimal weight: 30.0000 chunk 219 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 390 HIS A 587 HIS A 670 ASN B 188 GLN C 62 ASN E 28 HIS E 88 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 828 HIS I1112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.157440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117959 restraints weight = 40722.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115587 restraints weight = 29531.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117281 restraints weight = 25224.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117572 restraints weight = 20249.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117911 restraints weight = 16895.606| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25545 Z= 0.166 Angle : 0.580 11.103 34678 Z= 0.299 Chirality : 0.043 0.407 3998 Planarity : 0.004 0.076 4359 Dihedral : 5.428 57.992 3684 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 5.19 % Allowed : 25.74 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3085 helix: 1.84 (0.15), residues: 1275 sheet: 0.54 (0.23), residues: 514 loop : -1.56 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 791 TYR 0.019 0.001 TYR G 75 PHE 0.016 0.001 PHE I 204 TRP 0.019 0.001 TRP I1187 HIS 0.005 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (25538) covalent geometry : angle 0.57653 / 0.30 (34657) hydrogen bonds : bond 0.05359 / 3.60 ( 1215) hydrogen bonds : angle 4.36116 / 3.07 ( 3522) link_BETA1-4 : bond 0.00527 / 0.28 ( 1) link_BETA1-4 : angle 2.10740 / 1.14 ( 3) link_NAG-ASN : bond 0.00506 / 0.20 ( 6) link_NAG-ASN : angle 2.65747 / 1.77 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 577 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.6766 (mp0) cc_final: 0.6343 (mp0) REVERT: A 335 LYS cc_start: 0.8284 (mmtp) cc_final: 0.8060 (mmtm) REVERT: A 457 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7475 (mmmt) REVERT: A 460 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7323 (tmm) REVERT: A 480 ASP cc_start: 0.7457 (t0) cc_final: 0.7131 (t70) REVERT: A 500 GLU cc_start: 0.7199 (pm20) cc_final: 0.6769 (pm20) REVERT: A 594 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7585 (mm-40) REVERT: A 697 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8101 (m) REVERT: B 39 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.7050 (mtmm) REVERT: B 55 GLU cc_start: 0.7800 (tt0) cc_final: 0.7368 (tt0) REVERT: B 83 GLU cc_start: 0.6963 (mp0) cc_final: 0.6709 (mp0) REVERT: B 118 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 136 ILE cc_start: 0.8224 (mm) cc_final: 0.7989 (mt) REVERT: B 144 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.7711 (p) REVERT: B 147 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7725 (p) REVERT: B 280 LYS cc_start: 0.7241 (tttp) cc_final: 0.6961 (tttp) REVERT: C 26 LYS cc_start: 0.8238 (ttmm) cc_final: 0.7948 (ttmm) REVERT: C 82 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5723 (tt) REVERT: C 143 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7749 (p90) REVERT: C 225 MET cc_start: 0.5854 (mtm) cc_final: 0.5167 (mmm) REVERT: D 12 HIS cc_start: 0.8216 (m170) cc_final: 0.7920 (m90) REVERT: D 22 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7464 (m-80) REVERT: D 25 GLN cc_start: 0.7136 (mp10) cc_final: 0.6783 (mp10) REVERT: D 93 MET cc_start: 0.6280 (mmm) cc_final: 0.5589 (tmm) REVERT: D 143 MET cc_start: 0.7141 (mtm) cc_final: 0.6795 (mtm) REVERT: E 127 LYS cc_start: 0.8048 (tttt) cc_final: 0.7538 (tttt) REVERT: F 58 ASN cc_start: 0.7926 (m-40) cc_final: 0.7715 (m-40) REVERT: F 93 ILE cc_start: 0.8267 (tt) cc_final: 0.7982 (tp) REVERT: G 4 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7754 (mmt180) REVERT: G 111 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7549 (ttt180) REVERT: G 145 ARG cc_start: 0.8308 (mtp180) cc_final: 0.8052 (mtt180) REVERT: H 61 CYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6825 (t) REVERT: H 86 LYS cc_start: 0.7672 (mtpt) cc_final: 0.7290 (mtpp) REVERT: H 92 TYR cc_start: 0.8512 (t80) cc_final: 0.8291 (t80) REVERT: H 93 ASP cc_start: 0.7891 (t0) cc_final: 0.7432 (t0) REVERT: I 82 LYS cc_start: 0.7774 (pttm) cc_final: 0.7519 (pttm) REVERT: I 206 VAL cc_start: 0.7454 (m) cc_final: 0.7181 (t) REVERT: I 244 LYS cc_start: 0.8132 (tppt) cc_final: 0.7800 (tppt) REVERT: I 245 GLU cc_start: 0.7242 (tp30) cc_final: 0.6851 (tp30) REVERT: I 260 ARG cc_start: 0.7493 (tpp80) cc_final: 0.7208 (tpp80) REVERT: I 471 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: I 608 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6501 (pm20) REVERT: I 625 TYR cc_start: 0.6808 (OUTLIER) cc_final: 0.6470 (p90) REVERT: I 774 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7292 (mm-30) REVERT: I 801 LEU cc_start: 0.7142 (tt) cc_final: 0.6567 (tp) REVERT: I 813 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6874 (tpp) REVERT: I 843 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7448 (mmtm) REVERT: I 849 ARG cc_start: 0.7796 (ttp-110) cc_final: 0.7539 (ptp-110) REVERT: I 853 MET cc_start: 0.7628 (tmm) cc_final: 0.7413 (tmm) REVERT: I 855 MET cc_start: 0.7620 (tmm) cc_final: 0.7294 (tmm) REVERT: I 859 LYS cc_start: 0.7164 (tptt) cc_final: 0.6772 (pttm) REVERT: I 974 VAL cc_start: 0.7549 (t) cc_final: 0.7260 (m) REVERT: I 1082 LYS cc_start: 0.6986 (tppt) cc_final: 0.6589 (ttmm) REVERT: I 1117 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: I 1127 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6288 (mtm110) outliers start: 143 outliers final: 102 residues processed: 655 average time/residue: 0.1698 time to fit residues: 177.3291 Evaluate side-chains 687 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 568 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 61 CYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 205 GLN Chi-restraints excluded: chain I residue 237 PHE Chi-restraints excluded: chain I residue 271 GLU Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain I residue 398 GLU Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 427 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 469 CYS Chi-restraints excluded: chain I residue 471 GLU Chi-restraints excluded: chain I residue 475 ILE Chi-restraints excluded: chain I residue 481 ILE Chi-restraints excluded: chain I residue 608 GLU Chi-restraints excluded: chain I residue 625 TYR Chi-restraints excluded: chain I residue 695 MET Chi-restraints excluded: chain I residue 705 VAL Chi-restraints excluded: chain I residue 754 HIS Chi-restraints excluded: chain I residue 800 LEU Chi-restraints excluded: chain I residue 813 MET Chi-restraints excluded: chain I residue 824 LEU Chi-restraints excluded: chain I residue 966 SER Chi-restraints excluded: chain I residue 983 CYS Chi-restraints excluded: chain I residue 988 THR Chi-restraints excluded: chain I residue 1000 LEU Chi-restraints excluded: chain I residue 1007 SER Chi-restraints excluded: chain I residue 1032 PHE Chi-restraints excluded: chain I residue 1048 ARG Chi-restraints excluded: chain I residue 1117 PHE Chi-restraints excluded: chain I residue 1127 ARG Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1163 LYS Chi-restraints excluded: chain I residue 1186 SER Chi-restraints excluded: chain I residue 1191 HIS Chi-restraints excluded: chain I residue 1196 PHE Chi-restraints excluded: chain I residue 1198 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 169 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 286 optimal weight: 0.9980 chunk 253 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 GLN A 111 HIS A 670 ASN C 62 ASN E 28 HIS E 88 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 828 HIS I1112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.157259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117614 restraints weight = 40595.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115518 restraints weight = 28459.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117264 restraints weight = 23935.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117532 restraints weight = 18559.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117897 restraints weight = 16131.614| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25545 Z= 0.170 Angle : 0.584 13.583 34678 Z= 0.300 Chirality : 0.043 0.405 3998 Planarity : 0.004 0.051 4359 Dihedral : 5.396 56.839 3684 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 5.23 % Allowed : 26.10 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3085 helix: 1.81 (0.15), residues: 1281 sheet: 0.54 (0.23), residues: 517 loop : -1.58 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 791 TYR 0.019 0.001 TYR G 75 PHE 0.016 0.001 PHE F 26 TRP 0.023 0.001 TRP D 9 HIS 0.008 0.001 HIS E 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (25538) covalent geometry : angle 0.58056 / 0.30 (34657) hydrogen bonds : bond 0.05403 / 3.63 ( 1215) hydrogen bonds : angle 4.34867 / 3.06 ( 3522) link_BETA1-4 : bond 0.00546 / 0.29 ( 1) link_BETA1-4 : angle 2.12444 / 1.15 ( 3) link_NAG-ASN : bond 0.00480 / 0.18 ( 6) link_NAG-ASN : angle 2.63377 / 1.79 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 576 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8225 (mmtm) REVERT: A 182 GLU cc_start: 0.6775 (mp0) cc_final: 0.6370 (mp0) REVERT: A 335 LYS cc_start: 0.8284 (mmtp) cc_final: 0.8074 (mmtm) REVERT: A 457 LYS cc_start: 0.8013 (mmmt) cc_final: 0.7589 (mmmt) REVERT: A 460 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7351 (tmm) REVERT: A 480 ASP cc_start: 0.7441 (t0) cc_final: 0.7118 (t70) REVERT: A 500 GLU cc_start: 0.7204 (pm20) cc_final: 0.6723 (pm20) REVERT: A 594 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7581 (mm-40) REVERT: A 697 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8099 (m) REVERT: A 744 ILE cc_start: 0.8552 (mm) cc_final: 0.7886 (tt) REVERT: B 39 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7099 (mtmm) REVERT: B 55 GLU cc_start: 0.7761 (tt0) cc_final: 0.7500 (tt0) REVERT: B 118 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7536 (mm-30) REVERT: B 136 ILE cc_start: 0.8229 (mm) cc_final: 0.8007 (mt) REVERT: B 144 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7729 (p) REVERT: B 147 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7705 (p) REVERT: B 277 SER cc_start: 0.8392 (t) cc_final: 0.8165 (t) REVERT: B 280 LYS cc_start: 0.7370 (tttp) cc_final: 0.7124 (tttp) REVERT: C 26 LYS cc_start: 0.8229 (ttmm) cc_final: 0.7940 (ttmm) REVERT: C 82 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5703 (tt) REVERT: C 143 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7719 (p90) REVERT: C 225 MET cc_start: 0.5826 (mtm) cc_final: 0.5113 (mmm) REVERT: D 12 HIS cc_start: 0.8263 (m170) cc_final: 0.7953 (m90) REVERT: D 22 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: D 25 GLN cc_start: 0.7130 (mp10) cc_final: 0.6788 (mp10) REVERT: D 93 MET cc_start: 0.6275 (mmm) cc_final: 0.5595 (tmm) REVERT: D 143 MET cc_start: 0.7116 (mtm) cc_final: 0.6782 (mtm) REVERT: E 127 LYS cc_start: 0.7970 (tttt) cc_final: 0.7575 (tttt) REVERT: F 58 ASN cc_start: 0.8119 (m-40) cc_final: 0.7855 (m-40) REVERT: F 93 ILE cc_start: 0.8241 (tt) cc_final: 0.7959 (tp) REVERT: G 4 ARG cc_start: 0.8124 (mmm160) cc_final: 0.7748 (mmt180) REVERT: G 111 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7567 (ttt180) REVERT: G 145 ARG cc_start: 0.8319 (mtp180) cc_final: 0.8057 (mtt180) REVERT: H 61 CYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6887 (t) REVERT: H 86 LYS cc_start: 0.7664 (mtpt) cc_final: 0.7280 (mtpp) REVERT: H 93 ASP cc_start: 0.7837 (t0) cc_final: 0.7552 (t0) REVERT: I 72 MET cc_start: 0.7609 (ttp) cc_final: 0.7339 (tmm) REVERT: I 82 LYS cc_start: 0.7766 (pttm) cc_final: 0.7520 (pttm) REVERT: I 206 VAL cc_start: 0.7482 (m) cc_final: 0.7212 (t) REVERT: I 244 LYS cc_start: 0.8157 (tppt) cc_final: 0.7746 (tppt) REVERT: I 245 GLU cc_start: 0.7258 (tp30) cc_final: 0.6853 (tp30) REVERT: I 260 ARG cc_start: 0.7474 (tpp80) cc_final: 0.7201 (tpp80) REVERT: I 471 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7392 (pm20) REVERT: I 625 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6468 (p90) REVERT: I 710 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6722 (pt0) REVERT: I 734 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6830 (t80) REVERT: I 801 LEU cc_start: 0.7135 (tt) cc_final: 0.6578 (tp) REVERT: I 813 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6858 (tpp) REVERT: I 824 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7041 (mp) REVERT: I 843 LYS cc_start: 0.7914 (mmtm) cc_final: 0.7459 (mmtm) REVERT: I 849 ARG cc_start: 0.7771 (ttp-110) cc_final: 0.7531 (ptp-110) REVERT: I 853 MET cc_start: 0.7675 (tmm) cc_final: 0.7442 (tmm) REVERT: I 855 MET cc_start: 0.7612 (tmm) cc_final: 0.7281 (tmm) REVERT: I 859 LYS cc_start: 0.7163 (tptt) cc_final: 0.6754 (pttm) REVERT: I 1082 LYS cc_start: 0.6994 (tppt) cc_final: 0.6593 (ttmm) REVERT: I 1117 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7773 (m-80) REVERT: I 1127 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6433 (mtm180) outliers start: 144 outliers final: 103 residues processed: 654 average time/residue: 0.1657 time to fit residues: 172.7338 Evaluate side-chains 690 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 567 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 61 CYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 271 GLU Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain I residue 398 GLU Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 427 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 469 CYS Chi-restraints excluded: chain I residue 471 GLU Chi-restraints excluded: chain I residue 475 ILE Chi-restraints excluded: chain I residue 481 ILE Chi-restraints excluded: chain I residue 625 TYR Chi-restraints excluded: chain I residue 695 MET Chi-restraints excluded: chain I residue 705 VAL Chi-restraints excluded: chain I residue 710 GLU Chi-restraints excluded: chain I residue 734 PHE Chi-restraints excluded: chain I residue 754 HIS Chi-restraints excluded: chain I residue 800 LEU Chi-restraints excluded: chain I residue 813 MET Chi-restraints excluded: chain I residue 824 LEU Chi-restraints excluded: chain I residue 966 SER Chi-restraints excluded: chain I residue 983 CYS Chi-restraints excluded: chain I residue 988 THR Chi-restraints excluded: chain I residue 1000 LEU Chi-restraints excluded: chain I residue 1007 SER Chi-restraints excluded: chain I residue 1028 LEU Chi-restraints excluded: chain I residue 1032 PHE Chi-restraints excluded: chain I residue 1048 ARG Chi-restraints excluded: chain I residue 1102 ASN Chi-restraints excluded: chain I residue 1117 PHE Chi-restraints excluded: chain I residue 1127 ARG Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1163 LYS Chi-restraints excluded: chain I residue 1186 SER Chi-restraints excluded: chain I residue 1191 HIS Chi-restraints excluded: chain I residue 1196 PHE Chi-restraints excluded: chain I residue 1198 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 51 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 305 optimal weight: 4.9990 chunk 283 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 302 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 587 HIS A 670 ASN A 750 ASN C 62 ASN D 182 ASN E 28 HIS E 88 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 828 HIS I1112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.156622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116729 restraints weight = 40499.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114774 restraints weight = 28812.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115796 restraints weight = 24198.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116350 restraints weight = 20137.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116642 restraints weight = 16990.556| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25545 Z= 0.194 Angle : 0.608 12.532 34678 Z= 0.314 Chirality : 0.044 0.402 3998 Planarity : 0.004 0.053 4359 Dihedral : 5.402 58.457 3682 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 5.19 % Allowed : 26.72 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3085 helix: 1.72 (0.15), residues: 1288 sheet: 0.53 (0.23), residues: 520 loop : -1.69 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 247 TYR 0.022 0.002 TYR G 75 PHE 0.018 0.001 PHE F 26 TRP 0.033 0.002 TRP D 9 HIS 0.009 0.001 HIS E 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (25538) covalent geometry : angle 0.60517 / 0.31 (34657) hydrogen bonds : bond 0.05751 / 3.86 ( 1215) hydrogen bonds : angle 4.38768 / 3.09 ( 3522) link_BETA1-4 : bond 0.00311 / 0.16 ( 1) link_BETA1-4 : angle 2.15486 / 1.16 ( 3) link_NAG-ASN : bond 0.00409 / 0.16 ( 6) link_NAG-ASN : angle 2.58348 / 1.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 585 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8218 (mmtm) REVERT: A 182 GLU cc_start: 0.6753 (mp0) cc_final: 0.6369 (mp0) REVERT: A 356 LEU cc_start: 0.7904 (mp) cc_final: 0.7701 (mt) REVERT: A 460 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7348 (tmm) REVERT: A 480 ASP cc_start: 0.7436 (t0) cc_final: 0.7108 (t70) REVERT: A 500 GLU cc_start: 0.7194 (pm20) cc_final: 0.6771 (pm20) REVERT: A 594 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7596 (mm-40) REVERT: A 697 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8114 (m) REVERT: A 744 ILE cc_start: 0.8559 (mm) cc_final: 0.7902 (tt) REVERT: B 39 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7144 (mtmm) REVERT: B 55 GLU cc_start: 0.7782 (tt0) cc_final: 0.7481 (tt0) REVERT: B 118 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7543 (mm-30) REVERT: B 136 ILE cc_start: 0.8260 (mm) cc_final: 0.8011 (mt) REVERT: B 144 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7748 (p) REVERT: B 147 SER cc_start: 0.8134 (OUTLIER) cc_final: 0.7743 (p) REVERT: B 210 GLU cc_start: 0.7456 (tp30) cc_final: 0.7230 (tt0) REVERT: B 277 SER cc_start: 0.8465 (t) cc_final: 0.8247 (t) REVERT: C 82 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5926 (tt) REVERT: C 143 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7720 (p90) REVERT: C 225 MET cc_start: 0.5834 (mtm) cc_final: 0.5504 (mtm) REVERT: D 12 HIS cc_start: 0.8344 (m170) cc_final: 0.8062 (m90) REVERT: D 25 GLN cc_start: 0.7145 (mp10) cc_final: 0.6833 (mp10) REVERT: D 93 MET cc_start: 0.6324 (mmm) cc_final: 0.5672 (tmm) REVERT: D 143 MET cc_start: 0.7142 (mtm) cc_final: 0.6918 (mtm) REVERT: E 59 LEU cc_start: 0.8314 (mp) cc_final: 0.8082 (mp) REVERT: E 127 LYS cc_start: 0.7961 (tttt) cc_final: 0.7588 (tttt) REVERT: F 58 ASN cc_start: 0.8179 (m-40) cc_final: 0.7945 (m-40) REVERT: F 93 ILE cc_start: 0.8236 (tt) cc_final: 0.7946 (tp) REVERT: G 4 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7743 (mmt180) REVERT: G 111 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7640 (ttt180) REVERT: G 145 ARG cc_start: 0.8328 (mtp180) cc_final: 0.8060 (mtt180) REVERT: H 61 CYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6911 (t) REVERT: H 86 LYS cc_start: 0.7668 (mtpt) cc_final: 0.7288 (mtpp) REVERT: H 93 ASP cc_start: 0.7818 (t0) cc_final: 0.7485 (t0) REVERT: I 72 MET cc_start: 0.7625 (ttp) cc_final: 0.7363 (tmm) REVERT: I 82 LYS cc_start: 0.7795 (pttm) cc_final: 0.7459 (pttm) REVERT: I 131 GLN cc_start: 0.8127 (tp40) cc_final: 0.7648 (mm-40) REVERT: I 206 VAL cc_start: 0.7523 (m) cc_final: 0.7251 (t) REVERT: I 244 LYS cc_start: 0.8214 (tppt) cc_final: 0.7853 (tppt) REVERT: I 245 GLU cc_start: 0.7246 (tp30) cc_final: 0.6853 (tp30) REVERT: I 260 ARG cc_start: 0.7463 (tpp80) cc_final: 0.7187 (tpp80) REVERT: I 471 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: I 625 TYR cc_start: 0.6809 (OUTLIER) cc_final: 0.6470 (p90) REVERT: I 710 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6518 (pt0) REVERT: I 780 ARG cc_start: 0.6316 (tpp-160) cc_final: 0.5709 (ttm-80) REVERT: I 801 LEU cc_start: 0.7198 (tt) cc_final: 0.6713 (tp) REVERT: I 813 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6894 (tpp) REVERT: I 843 LYS cc_start: 0.7923 (mmtm) cc_final: 0.7457 (mmtm) REVERT: I 849 ARG cc_start: 0.7792 (ttp-110) cc_final: 0.7528 (ptp-110) REVERT: I 853 MET cc_start: 0.7711 (tmm) cc_final: 0.7452 (tmm) REVERT: I 855 MET cc_start: 0.7600 (tmm) cc_final: 0.7300 (tmm) REVERT: I 859 LYS cc_start: 0.7178 (tptt) cc_final: 0.6774 (pttm) REVERT: I 1082 LYS cc_start: 0.7021 (tppt) cc_final: 0.6625 (ttmm) REVERT: I 1117 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: I 1127 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6439 (mtm180) REVERT: I 1174 LYS cc_start: 0.6882 (mttp) cc_final: 0.6609 (mtmt) outliers start: 143 outliers final: 106 residues processed: 657 average time/residue: 0.1635 time to fit residues: 171.8182 Evaluate side-chains 695 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 572 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 61 CYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 271 GLU Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain I residue 398 GLU Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 427 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 438 ILE Chi-restraints excluded: chain I residue 469 CYS Chi-restraints excluded: chain I residue 471 GLU Chi-restraints excluded: chain I residue 475 ILE Chi-restraints excluded: chain I residue 481 ILE Chi-restraints excluded: chain I residue 625 TYR Chi-restraints excluded: chain I residue 695 MET Chi-restraints excluded: chain I residue 710 GLU Chi-restraints excluded: chain I residue 734 PHE Chi-restraints excluded: chain I residue 754 HIS Chi-restraints excluded: chain I residue 800 LEU Chi-restraints excluded: chain I residue 813 MET Chi-restraints excluded: chain I residue 966 SER Chi-restraints excluded: chain I residue 983 CYS Chi-restraints excluded: chain I residue 988 THR Chi-restraints excluded: chain I residue 1000 LEU Chi-restraints excluded: chain I residue 1007 SER Chi-restraints excluded: chain I residue 1028 LEU Chi-restraints excluded: chain I residue 1032 PHE Chi-restraints excluded: chain I residue 1048 ARG Chi-restraints excluded: chain I residue 1102 ASN Chi-restraints excluded: chain I residue 1117 PHE Chi-restraints excluded: chain I residue 1127 ARG Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1163 LYS Chi-restraints excluded: chain I residue 1191 HIS Chi-restraints excluded: chain I residue 1196 PHE Chi-restraints excluded: chain I residue 1198 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 6 optimal weight: 0.2980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 GLN A 111 HIS A 670 ASN B 279 ASN C 62 ASN E 28 HIS E 88 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.156723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116802 restraints weight = 40746.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114927 restraints weight = 28739.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116173 restraints weight = 23686.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116602 restraints weight = 19331.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117067 restraints weight = 16519.325| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25545 Z= 0.198 Angle : 0.621 12.231 34678 Z= 0.319 Chirality : 0.044 0.400 3998 Planarity : 0.004 0.052 4359 Dihedral : 5.410 57.674 3682 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.36 % Rotamer: Outliers : 5.01 % Allowed : 27.26 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 3085 helix: 1.66 (0.15), residues: 1290 sheet: 0.63 (0.23), residues: 508 loop : -1.72 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 247 TYR 0.022 0.002 TYR G 75 PHE 0.018 0.001 PHE I 204 TRP 0.042 0.002 TRP D 9 HIS 0.007 0.001 HIS E 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (25538) covalent geometry : angle 0.61841 / 0.32 (34657) hydrogen bonds : bond 0.05756 / 3.87 ( 1215) hydrogen bonds : angle 4.40232 / 3.10 ( 3522) link_BETA1-4 : bond 0.00489 / 0.26 ( 1) link_BETA1-4 : angle 2.02022 / 1.09 ( 3) link_NAG-ASN : bond 0.00398 / 0.15 ( 6) link_NAG-ASN : angle 2.55189 / 1.79 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 583 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8190 (mmtm) REVERT: A 182 GLU cc_start: 0.6752 (mp0) cc_final: 0.6376 (mp0) REVERT: A 457 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7617 (mmmt) REVERT: A 460 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7355 (tmm) REVERT: A 480 ASP cc_start: 0.7438 (t0) cc_final: 0.7108 (t70) REVERT: A 500 GLU cc_start: 0.7108 (pm20) cc_final: 0.6785 (pm20) REVERT: A 594 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7584 (mm-40) REVERT: A 697 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8119 (m) REVERT: A 744 ILE cc_start: 0.8557 (mm) cc_final: 0.7907 (tt) REVERT: B 39 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7158 (mtmm) REVERT: B 55 GLU cc_start: 0.7763 (tt0) cc_final: 0.7510 (tt0) REVERT: B 118 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7494 (mm-30) REVERT: B 136 ILE cc_start: 0.8257 (mm) cc_final: 0.8039 (mt) REVERT: B 144 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7742 (p) REVERT: B 147 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7733 (p) REVERT: B 210 GLU cc_start: 0.7452 (tp30) cc_final: 0.7229 (tt0) REVERT: B 277 SER cc_start: 0.8473 (t) cc_final: 0.8271 (t) REVERT: C 82 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5902 (tt) REVERT: C 143 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7713 (p90) REVERT: C 225 MET cc_start: 0.5858 (mtm) cc_final: 0.5519 (mtm) REVERT: D 12 HIS cc_start: 0.8341 (m170) cc_final: 0.8036 (m90) REVERT: D 25 GLN cc_start: 0.7146 (mp10) cc_final: 0.6841 (mp10) REVERT: D 93 MET cc_start: 0.6326 (mmm) cc_final: 0.5675 (tmm) REVERT: D 143 MET cc_start: 0.7142 (mtm) cc_final: 0.6915 (mtm) REVERT: E 127 LYS cc_start: 0.7958 (tttt) cc_final: 0.7593 (tttt) REVERT: F 58 ASN cc_start: 0.8177 (m-40) cc_final: 0.7910 (m-40) REVERT: F 93 ILE cc_start: 0.8229 (tt) cc_final: 0.7958 (tp) REVERT: G 4 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7745 (mmt180) REVERT: G 11 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7919 (mp) REVERT: G 93 LYS cc_start: 0.8202 (tttt) cc_final: 0.7858 (tttp) REVERT: G 111 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7633 (ttt180) REVERT: G 145 ARG cc_start: 0.8323 (mtp180) cc_final: 0.8051 (mtt180) REVERT: H 61 CYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6961 (t) REVERT: H 86 LYS cc_start: 0.7666 (mtpt) cc_final: 0.7285 (mtpp) REVERT: I 72 MET cc_start: 0.7598 (ttp) cc_final: 0.7336 (tmm) REVERT: I 82 LYS cc_start: 0.7784 (pttm) cc_final: 0.7442 (pttm) REVERT: I 131 GLN cc_start: 0.8113 (tp40) cc_final: 0.7642 (mm-40) REVERT: I 206 VAL cc_start: 0.7525 (m) cc_final: 0.7262 (t) REVERT: I 244 LYS cc_start: 0.8192 (tppt) cc_final: 0.7843 (tppt) REVERT: I 245 GLU cc_start: 0.7221 (tp30) cc_final: 0.6832 (tp30) REVERT: I 260 ARG cc_start: 0.7453 (tpp80) cc_final: 0.7187 (tpp80) REVERT: I 335 LYS cc_start: 0.8057 (mtpp) cc_final: 0.7750 (mmmm) REVERT: I 471 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: I 625 TYR cc_start: 0.6819 (OUTLIER) cc_final: 0.6477 (p90) REVERT: I 710 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6678 (pt0) REVERT: I 801 LEU cc_start: 0.7208 (tt) cc_final: 0.6716 (tp) REVERT: I 807 MET cc_start: 0.7598 (mmm) cc_final: 0.7374 (mmm) REVERT: I 813 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6852 (tpp) REVERT: I 828 HIS cc_start: 0.7256 (m170) cc_final: 0.6973 (m-70) REVERT: I 843 LYS cc_start: 0.7928 (mmtm) cc_final: 0.7462 (mmtm) REVERT: I 849 ARG cc_start: 0.7789 (ttp-110) cc_final: 0.7518 (ptp-110) REVERT: I 853 MET cc_start: 0.7709 (tmm) cc_final: 0.7452 (tmm) REVERT: I 855 MET cc_start: 0.7565 (tmm) cc_final: 0.7276 (tmm) REVERT: I 859 LYS cc_start: 0.7181 (tptt) cc_final: 0.6769 (pttm) REVERT: I 1082 LYS cc_start: 0.7030 (tppt) cc_final: 0.6625 (ttmm) REVERT: I 1117 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: I 1127 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6421 (mtp180) outliers start: 138 outliers final: 100 residues processed: 651 average time/residue: 0.1642 time to fit residues: 171.8008 Evaluate side-chains 699 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 581 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 61 CYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 271 GLU Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain I residue 398 GLU Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 427 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 438 ILE Chi-restraints excluded: chain I residue 469 CYS Chi-restraints excluded: chain I residue 471 GLU Chi-restraints excluded: chain I residue 475 ILE Chi-restraints excluded: chain I residue 481 ILE Chi-restraints excluded: chain I residue 625 TYR Chi-restraints excluded: chain I residue 695 MET Chi-restraints excluded: chain I residue 710 GLU Chi-restraints excluded: chain I residue 734 PHE Chi-restraints excluded: chain I residue 754 HIS Chi-restraints excluded: chain I residue 800 LEU Chi-restraints excluded: chain I residue 813 MET Chi-restraints excluded: chain I residue 966 SER Chi-restraints excluded: chain I residue 983 CYS Chi-restraints excluded: chain I residue 988 THR Chi-restraints excluded: chain I residue 1000 LEU Chi-restraints excluded: chain I residue 1007 SER Chi-restraints excluded: chain I residue 1032 PHE Chi-restraints excluded: chain I residue 1102 ASN Chi-restraints excluded: chain I residue 1117 PHE Chi-restraints excluded: chain I residue 1127 ARG Chi-restraints excluded: chain I residue 1163 LYS Chi-restraints excluded: chain I residue 1191 HIS Chi-restraints excluded: chain I residue 1196 PHE Chi-restraints excluded: chain I residue 1198 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 238 optimal weight: 1.9990 chunk 293 optimal weight: 0.0270 chunk 27 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 282 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 154 optimal weight: 0.9990 chunk 10 optimal weight: 0.0170 chunk 82 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 670 ASN C 62 ASN D 25 GLN E 28 HIS E 88 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1112 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.158239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117817 restraints weight = 40682.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116184 restraints weight = 29392.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116872 restraints weight = 23960.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117792 restraints weight = 20088.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117989 restraints weight = 18259.593| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25545 Z= 0.129 Angle : 0.600 14.151 34678 Z= 0.305 Chirality : 0.042 0.382 3998 Planarity : 0.004 0.049 4359 Dihedral : 5.238 55.915 3682 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 3.52 % Allowed : 28.75 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.15), residues: 3085 helix: 1.84 (0.15), residues: 1295 sheet: 0.59 (0.23), residues: 519 loop : -1.70 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 383 TYR 0.019 0.001 TYR I1075 PHE 0.018 0.001 PHE I 204 TRP 0.053 0.001 TRP D 9 HIS 0.007 0.001 HIS E 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (25538) covalent geometry : angle 0.59694 / 0.30 (34657) hydrogen bonds : bond 0.04849 / 3.26 ( 1215) hydrogen bonds : angle 4.27691 / 3.01 ( 3522) link_BETA1-4 : bond 0.00414 / 0.22 ( 1) link_BETA1-4 : angle 1.83662 / 0.98 ( 3) link_NAG-ASN : bond 0.00552 / 0.21 ( 6) link_NAG-ASN : angle 2.47557 / 1.75 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 566 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8226 (mmtm) REVERT: A 182 GLU cc_start: 0.6734 (mp0) cc_final: 0.6350 (mp0) REVERT: A 460 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7331 (tmm) REVERT: A 480 ASP cc_start: 0.7430 (t0) cc_final: 0.7089 (t70) REVERT: A 500 GLU cc_start: 0.7119 (pm20) cc_final: 0.6831 (pm20) REVERT: A 594 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7554 (mm-40) REVERT: A 697 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8105 (m) REVERT: A 744 ILE cc_start: 0.8541 (mm) cc_final: 0.7882 (tt) REVERT: B 55 GLU cc_start: 0.7696 (tt0) cc_final: 0.7476 (tt0) REVERT: B 118 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7462 (mm-30) REVERT: B 136 ILE cc_start: 0.8197 (mm) cc_final: 0.7978 (mt) REVERT: B 144 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7674 (p) REVERT: B 147 SER cc_start: 0.8048 (OUTLIER) cc_final: 0.7671 (p) REVERT: B 210 GLU cc_start: 0.7457 (tp30) cc_final: 0.7209 (tt0) REVERT: C 26 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7821 (ttmm) REVERT: C 82 LEU cc_start: 0.6163 (OUTLIER) cc_final: 0.5882 (tt) REVERT: C 225 MET cc_start: 0.5857 (mtm) cc_final: 0.5514 (mtm) REVERT: D 12 HIS cc_start: 0.8266 (m170) cc_final: 0.7863 (m-70) REVERT: D 93 MET cc_start: 0.6283 (mmm) cc_final: 0.5629 (tmm) REVERT: D 143 MET cc_start: 0.7138 (mtm) cc_final: 0.6913 (mtm) REVERT: E 59 LEU cc_start: 0.8323 (mp) cc_final: 0.8115 (mp) REVERT: E 127 LYS cc_start: 0.7945 (tttt) cc_final: 0.7593 (tttt) REVERT: F 58 ASN cc_start: 0.7937 (m-40) cc_final: 0.7685 (m-40) REVERT: G 4 ARG cc_start: 0.8137 (mmm160) cc_final: 0.7766 (mmt180) REVERT: G 11 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7805 (mp) REVERT: G 93 LYS cc_start: 0.8184 (tttt) cc_final: 0.7850 (tttp) REVERT: G 145 ARG cc_start: 0.8286 (mtp180) cc_final: 0.8022 (mtt180) REVERT: H 61 CYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6882 (t) REVERT: H 86 LYS cc_start: 0.7651 (mtpt) cc_final: 0.7266 (mtpp) REVERT: I 72 MET cc_start: 0.7590 (ttp) cc_final: 0.7210 (tmm) REVERT: I 82 LYS cc_start: 0.7762 (pttm) cc_final: 0.7485 (pttm) REVERT: I 131 GLN cc_start: 0.8113 (tp40) cc_final: 0.7648 (mm-40) REVERT: I 206 VAL cc_start: 0.7518 (m) cc_final: 0.7219 (t) REVERT: I 244 LYS cc_start: 0.8140 (tppt) cc_final: 0.7756 (tppt) REVERT: I 245 GLU cc_start: 0.7151 (tp30) cc_final: 0.6739 (tp30) REVERT: I 260 ARG cc_start: 0.7466 (tpp80) cc_final: 0.7190 (tpp80) REVERT: I 471 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7409 (pm20) REVERT: I 625 TYR cc_start: 0.6821 (OUTLIER) cc_final: 0.6488 (p90) REVERT: I 710 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6744 (pt0) REVERT: I 780 ARG cc_start: 0.6359 (tpp-160) cc_final: 0.5968 (ttm170) REVERT: I 801 LEU cc_start: 0.6986 (tt) cc_final: 0.6473 (tp) REVERT: I 813 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6808 (tpp) REVERT: I 828 HIS cc_start: 0.7255 (m170) cc_final: 0.7027 (m90) REVERT: I 843 LYS cc_start: 0.7896 (mmtm) cc_final: 0.7431 (mmtm) REVERT: I 849 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7529 (ptp-110) REVERT: I 853 MET cc_start: 0.7717 (tmm) cc_final: 0.7449 (tmm) REVERT: I 855 MET cc_start: 0.7591 (tmm) cc_final: 0.7282 (tmm) REVERT: I 859 LYS cc_start: 0.7158 (tptt) cc_final: 0.6761 (pttm) REVERT: I 1082 LYS cc_start: 0.6947 (tppt) cc_final: 0.6557 (ttmm) REVERT: I 1127 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6389 (mtp180) outliers start: 97 outliers final: 78 residues processed: 617 average time/residue: 0.1675 time to fit residues: 165.6287 Evaluate side-chains 653 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 561 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 28 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 61 CYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 271 GLU Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain I residue 398 GLU Chi-restraints excluded: chain I residue 406 LEU Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 427 ILE Chi-restraints excluded: chain I residue 469 CYS Chi-restraints excluded: chain I residue 471 GLU Chi-restraints excluded: chain I residue 475 ILE Chi-restraints excluded: chain I residue 481 ILE Chi-restraints excluded: chain I residue 625 TYR Chi-restraints excluded: chain I residue 695 MET Chi-restraints excluded: chain I residue 710 GLU Chi-restraints excluded: chain I residue 734 PHE Chi-restraints excluded: chain I residue 754 HIS Chi-restraints excluded: chain I residue 800 LEU Chi-restraints excluded: chain I residue 813 MET Chi-restraints excluded: chain I residue 966 SER Chi-restraints excluded: chain I residue 988 THR Chi-restraints excluded: chain I residue 1000 LEU Chi-restraints excluded: chain I residue 1007 SER Chi-restraints excluded: chain I residue 1032 PHE Chi-restraints excluded: chain I residue 1048 ARG Chi-restraints excluded: chain I residue 1102 ASN Chi-restraints excluded: chain I residue 1117 PHE Chi-restraints excluded: chain I residue 1127 ARG Chi-restraints excluded: chain I residue 1191 HIS Chi-restraints excluded: chain I residue 1196 PHE Chi-restraints excluded: chain I residue 1198 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 26 optimal weight: 2.9990 chunk 143 optimal weight: 0.4980 chunk 290 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 201 optimal weight: 0.0020 chunk 15 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 503 HIS A 670 ASN C 62 ASN E 28 HIS E 88 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1112 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118646 restraints weight = 40587.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116876 restraints weight = 29484.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118033 restraints weight = 24323.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118485 restraints weight = 18765.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118628 restraints weight = 17524.877| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25545 Z= 0.126 Angle : 0.594 12.245 34678 Z= 0.302 Chirality : 0.042 0.378 3998 Planarity : 0.004 0.049 4359 Dihedral : 5.171 55.398 3682 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.75 % Rotamer: Outliers : 3.52 % Allowed : 28.86 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3085 helix: 1.88 (0.14), residues: 1295 sheet: 0.63 (0.23), residues: 520 loop : -1.67 (0.16), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 383 TYR 0.021 0.001 TYR I1075 PHE 0.018 0.001 PHE I 204 TRP 0.055 0.001 TRP D 9 HIS 0.036 0.001 HIS E 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (25538) covalent geometry : angle 0.59112 / 0.30 (34657) hydrogen bonds : bond 0.04706 / 3.17 ( 1215) hydrogen bonds : angle 4.23906 / 2.98 ( 3522) link_BETA1-4 : bond 0.00619 / 0.33 ( 1) link_BETA1-4 : angle 1.66132 / 0.88 ( 3) link_NAG-ASN : bond 0.00516 / 0.19 ( 6) link_NAG-ASN : angle 2.42921 / 1.72 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4857.52 seconds wall clock time: 84 minutes 36.16 seconds (5076.16 seconds total)